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opencc-zeroMar 2020View details →

Development and testing of a novel Killer-Rescue self-limiting gene drive system in Drosophila melanogaster

Here we report the development and testing of a novel self-limiting gene drive system, Killer-Rescue, in Drosophila melanogaster. This system is composed of an auto-regulated Gal4 Killer (K) and a Gal4-activated Gal80 Rescue (R). Overexpression of Gal4 is lethal, but in the presence of R activation of Gal80 leads to much lower levels of Gal4 and rescue of lethality. We demonstrate that with a single 2:1 engineered to wildtype release, K drives R through the population and after nine generations more than 98% of the population carry R and less than 2% of the population are wildtype flies. We discuss how this simple Killer-Rescue gene drive system may be readily adapted for population replacement in a human health pest, Aedes aegypti, or for population suppression in an agricultural pest, Drosophila suzukii.

opencc-zeroAug 2020View details →

Vape flavorants dull sensory perception and cause hyperactivity in developing zebrafish embryos

E-cigarette use (vaping) during pregnancy has been increasing, and the potential exists for the developing brain in utero to be exposed to chemical constituents in the vape. Vapes come in over 7,000 unique flavors with and without nicotine, and while nicotine is a known neurotoxicant, the effects of vape flavoring alone, in the absence of nicotine, on brain function are not well understood. Here we performed a screen of vape aerosol extracts (VAEs) to determine the potential for prenatal neurotoxicity using the zebrafish embryo photomotor response (PMR) – a translational biosensor of neurobehavioral effects. We screened three commonly used aerosolized vape liquids (flavored and flavorless) either with or without nicotine. No neurobehavioral effects were detected in flavorless, nicotine-free VAEs, while the addition of nicotine to this VAE dulled sensory perception. Flavored nicotine-free VAEs also dulled sensory perception and caused hyperactivity in zebrafish embryos. The combination of flavor and nicotine produced largely additive effects. Flavored VAEs without nicotine had similar neuroactive potency as nicotine. Similar effects were also seen in embryos exposed to the pure flavoring compound, cinnamaldehyde. Together, using zebrafish PMR as a high throughput translational behavioral model for prenatal exposure, our results demonstrate that e-cigarette flavorants that we screened elicit neurobehavioral effects worthy of further investigation for long-term neurotoxic potential, and also have the potential to modulate nicotine impact on the developing brain.

opencc-zeroAug 2020View details →

Data from: Developing extruded seed pellets to overcome soil hydrophobicity and seedling emergence barriers

Globally soil water repellency is a major constraint to plant establishment, restricting water infiltration and moisture retention in the seed zone, resulting in poor germination and seedling emergence. To address this problem within an ecosystem restoration context, we investigated the use of a surfactant in extruded seed pellets to improve native plant recruitment in water repellent topsoils of two proteaceous woodland species, Banksia menziesii R.Br (glasshouse trial) and Lambertia inermis R.Br (field trial). In this two-part study, we first examined B. menziesii seedling performance in detail under glasshouse conditions for differences in survival between the extruded pelleting formulations after an induced drought at 12 weeks. We demonstrated that there was no difference in seedling emergence, amongst control seed and pellet treatments in B. menziesii. Initially B. menziesii seedlings emerged faster in the control treatment (non-pelleted control seeds) and had greater initial plant growth (leaf and root production), however by week 12, seedlings generated from pellets were not significantly different from the control seeds, and pellets + surfactant had the greatest number of leaf establishment. Survival after drought of B. menziesii seedlings ranged from 14 to 31 days with pellet + surfactant surviving approximately 2.6 days (11.8%) longer than the control seeds. For the second species, L. inermis, seedling emergence under field conditions was approximately 24% greater in seedlings derived from extruded pellets, however there was no difference in overall survival due to post-emergence predation. This study provides a proof of concept that seedling emergence in water repellent soils can be enhanced with extruded pellets containing surfactants. Our demonstration under in situ and ex situ conditions confirms the prospective use of seed enhancement technologies with future development and field-testing warranted.

opencc-zeroSep 2020View details →

Temperature-mediated tradeoff between development and performance in larval wood frogs (Rana sylvatica)

Countergradient variation has been detected in diverse taxa. In a common manifestation, individuals from colder environments develop faster than conspecifics from warmer environments when placed in a common garden. Where such a pattern exists, it implies a tradeoff: individuals from warmer environments have intrinsic rates of development lower than those demonstrated by other individuals of the same species. We explored a tradeoff between development rate and locomotor performance in the wood frog (Rana sylvatica), an amphibian for which countergradient variation has been well documented. We reared wood frogs from 10 populations under two temperature regimes, bracketing the temperatures observed in local natural ponds. Individuals reared under warmer conditions developed more rapidly but exhibited burst speeds 20% lower than individuals reared under colder conditions. The shape of the relationship was consistent across the 10 populations and thus, we found no evidence of countergradient variation in performance. Burst speed assays of wild-caught tadpoles from the same populations showed a similar but nonsignificant trend, with greater variability among ponds. Overall, our findings support the existence of a tradeoff that may be of broad importance and which may help explain widespread occurrence of countergradient variation.

opencc-zeroSep 2021View details →

Tool for genomic selection and breeding to evolutionary adaptation: Development of a 100K single nucleotide polymorphism array for the honey bee

High-throughput high density genotyping arrays continue to be a fast, accurate, and cost-effective method for genotyping thousands of polymorphisms in high numbers of individuals. Here we have developed a new high-density SNP genotyping array (103 270 SNPs) for honey bees, one of the most ecologically and economically important pollinators worldwide. SNPs were detected by conducting whole genome resequencing of 61 honey bee drones (haploid males) from throughout Europe. Selection of SNPs for the chip was done in multiple steps using several criteria. The majority of SNPs were selected based on their location within known candidate regions or genes underlying a range of honey bee traits, including hygienic behaviour against pathogens, foraging and subspecies. Additionally, markers from a GWAS of hygienic behaviour against the major honey bee parasite Varroa destructor, were brought over. The chip also includes SNPs associated with each of three major breeding objectives - honey yield, gentleness and Varroa resistance. We validated the chip and make recommendations for its use by determining error rates in repeat genotypings, examining the genotyping performance of different tissues, and by testing how well different sample types represent the queen's genotype. The latter is a key test because it is highly beneficial to be able to determine the queen's genotype by non-lethal means. The array is now publicly available and we suggest it will be a useful tool in genomic selection and honey bee breeding, as well as for GWAS of different traits, and for population genomic, adaptation and conservation questions.

opencc-zeroSep 2020View details →

Development and field evaluation of a motion sensor activated suction trap to study vector-host interactions

1. Researchers elucidating vectors of zoonotic diseases encounter problems with inefficient surveillance techniques leading to underestimation of the importance of some species, and the overestimation of the importance of others. Carbon dioxide-baited light traps are the most widely used traps for sampling vector groups. However aspirating directly from the hosts is the most accurate method to incriminate vectors. 2. A novel vector trapping system was developed, consisting of a suction trap, activated by a motion sensor, and controlled by a microcontroller, which activates automatically when host animals approach. The prototype was tested in two field experiments with ungulates and biting midges (Diptera: Ceratopogonidae) at a preserve in Florida. We measured the biting midge community collected at traps near and far from hosts and compared communities using diversity metrics and abundance curves. 3. Traps activated in the presence of host animals with 94% accuracy. Diversity and richness of Culicoides species differed between sensor and control traps with 11 species captured by control traps and 7 species by sensor traps. Vector species were captured in significantly greater numbers in sensor traps, while more non-vector species were caught in control traps. 4. Results confirm that vector species can be underrepresented in light trap collections, likely due to their tight associations with vertebrate hosts, a finding that should be taken into consideration when incriminating arbovirus vectors. Our novel trap system was a first attempt at solving the issue of collecting vector species from non-tame animals, effectively aspirating questing midges. Simple modifications of the system could be made to target other vector-host systems.

How Office Layouts Influence Software Development? (Apresentação em video)

Background: Organizations are constantly looking for performance improvements, and office layout has been widely studied because of its hypothetical influences on the social dynamics of software engineering projects. Aim: In this article, we investigate the perceived outcomes of different workspace characteristics, from the perspective of software engineering professionals. Methods: To achieve that, we conducted a survey with software engineering practitioners, and collected data on the perceptions about their current workspaces and performance from 47 participants. We used the results of a previous systematic review to design the survey questionnaire, and focused on the four human aspects known to be influenced by the office layout. Results: Different workspace settings exhibited similar perceptions in most of the investigated factors. However, we reveal 14 items that responsible for significant differences in the performance outcomes, such as communication quality, collaboration, team learning, privacy and others. In general, open spaces were the most effective office layout to enable all these factors. Conclusions: As a conclusion, our study demonstrates that there is not a generally accepted best model for software development workspace design, as all types of setting have positive and negative aspects. Organizations that are considering investing any budget in such things as radical workspace redesign should ponder the change very carefully. Also, there is still much room for investigation in this topic.

Developers eXperience (DX) in ALM software tools: an investigation on virtual kanban boards

Video de backup da apresentação do artigo "Developers eXperience (DX) in ALM software tools: an investigation on virtual kanban boards" no SBES 2020 - Trilha de Ideias Inovadoras e Resultados Emergentes.

Incremental Development of Safety Cases: a Mapping Study

Video presentation for Research Track article "Incremental Development of Safety Cases: a Mapping Study"

opencc-by-4.0Feb 2018View details →

When Testing Meets Code Review: Why and How Developers Review Tests (Appendix)

Dataset of "When Testing Meets Code Review: Why and How Developers Review Tests" This appendix material refers to the paper "When Testing Meets Code Review: Why and How Developers Review Tests" published in the Proceedings of the 40th International Conference on Software Engineering (ICSE 2018)

Dataset for "Appreciating our 60 years of life": Developing a transactional model of narrative identity and relationships experienced within an individualized, technological intervention for dementia care

Interview transcripts and participant information for “Appreciating our 60 years of life”: Developing a transactional model of narrative identity and relationships experienced within an individualized, technological intervention for dementia care.  Collected as part of the SENSE-GARDEN Multisite Trial (https://sense-garden.eu/). This work was supported by AAL under Grant AAL/Call2016/054-b/2017, co-funded by the European Commission and National Funding Agencies of Norway, Belgium, Romania, and Portugal.

Data from: Antibiotics in hives and their effects on honey bee physiology and behavioral development

Recurrent honey bee losses make it critical to understand the impact of human interventions, such as antibiotics use in apiculture. Antibiotics are used to prevent or treat bacterial infections in colonies. However, little is known about their effects on honey bee development. We studied the effect of two commercial beekeeping antibiotics on the bee physiology and behavior throughout development. Our results show that antibiotic treatments have an effect on amount of lipids and rate of behavioral development. Lipid amount in treated bees was higher than those not treated. Also, the timing of antibiotic treatment had distinct effects for the age of onset of behaviors starting with cleaning, then nursing and lastly foraging. Bees treated during larva-pupa stages demonstrated an accelerated behavioral development and loss of lipids, while bees treated from larva to adulthood had a delay in behavioral development and loss of lipids. The effects were shared across the two antibiotics tested, TerramycinR (oxytetracycline) and TylanR (tylosin tartrate). These results on effects of antibiotic treatments suggest a role of microbiota in the interaction between the fat body and brain that is important for honey bee behavioral development.

Teaching Development of Distributed Software during COVID-19: An experience report in Brazil

In 2020, the COVID-19 pandemic affected all sectors of society worldwide, including education. Due to the social isolation requirement, several educational institutions used the Emergency Remote Teaching (ERT) approach to keep their courses active, at least partially. This document provides an experience report about using ERT in two courses (Distributed Systems and Software Development for the Cloud) that deal with the Development of Distributed Software Systems. In these two courses, we used three main approaches: synchronous online classes, asynchronous learning videos, and online material available on a Git repository. In some classes, we also adopted active methodologies such as problem-based learning and flipped classroom. Students were evaluated by seminars, tests, and programming activities. In the end, we collected their feedback from an online survey. Forty-two (42) graduate and undergraduate students reported a good level of acceptance of our ERT model. Part of the students had difficulties in doing their programming homework, and the main obstacles reported by them were: (i) their psychological context and (ii) to reconcile the course activities with home tasks as well as the demands of their jobs. Once practical experiences in ERT will be essential for a while given the uncertainty about how long COVID-19 pandemic will remain active, we expect the highlights and drawbacks of our experience could help other professors in planning their courses.

Data from: Tek/Tie2 is not required for cardiovascular development in zebrafish

Angiopoietin/TIE signalling plays a major role in blood and lymphatic vessel development. In mouse, Tek/Tie2 mutants die prenatally due to a severely underdeveloped cardiovascular system. In contrast, in zebrafish, previous studies have reported that while embryos injected with tek morpholinos (MOs) exhibit severe vascular defects, tek mutants display no obvious vascular malformations. To further investigate the function of zebrafish Tek, we generated a panel of loss-of-function tek mutants, including RNA-less alleles, an allele lacking the MO-binding site, an in-frame deletion allele, and a premature termination codon-containing allele. Our data show that all these mutants survive to adulthood with no obvious cardiovascular defects. MO injections into tek mutants lacking the MO-binding site or the entire tek locus cause similar vascular defects as those observed in MO-injected +/+ siblings, indicating off-target effects of the MOs. Surprisingly, comprehensive phylogenetic profiling and synteny analyses reveal that Tek was lost in the largest teleost clade, suggesting a lineage-specific shift in the function of TEK during vertebrate evolution. Altogether, these data show that Tek is dispensable for zebrafish development, and probably dispensable in most teleost species.

The Evolving Nature of Developers' Contributions in Open Source Projects

Vídeo com a apresentação do artigo The Evolving Nature of Developers’ Contributions in Open Source Projects Autores: Talita Orfanó, Mariza Bigonha, Kecia Ferreira

opencc-by-4.0Mar 2020View details →

Development and evaluation of a test setup to investigate distance differences in immersive virtual environments

Nowadays, with recent advances in virtual reality technology, it is easily possible to integrate real objects into virtual environments by creating an exact virtual replication and enabling interaction with them by mapping the obtained tracking data of the real to the virtual objects. The primary goal of our study is to develop a system to investigate distance differences for near-field interaction in immersive virtual environments. In this context, the term distance difference refers to the shift between a real object and the respective replication of the real object in the virtual environment of the same size. This could occur for a number of reasons e.g. due to errors in motion tracking or mistakes in designing the virtual environment. Our virtual environment is developed using the Unity3D game engine, while the immersive contents were displayed on an HTC Vive Pro headmounted display. The virtual room shown to the user includes a replication of the real testing lab environment, while one of the two real objects is tracked and mirrored to the virtual world using an HTC Vive Tracker. Both objects are present in the real as well as in the virtual world. To find perceivable distance differences in the near-field, the actual task in the subjective test was to pick up one object and place it into another object. The position of the static object in the virtual world is shifted by values between 0 and 4 cm, while the position of the real object is kept constant. The system is evaluated by conducting a subjective proof-of-concept test with 18 test subjects. The distance difference is evaluated by the subjects through estimating perceived confusion on a modified 5-point absolute category rating scale. The study provides quantitative insights into allowable real-world vs. virtual-world mismatch boundaries for near-field interactions, with a threshold value of around 1 cm.

Joint Autoregressive and Graph Models for Software and Developer Social Networks

This zip contains three CSV files and one folder. This dataset contains information for the recent ten distributions. <ul> <li>developer_attributes.csv: There are seven columns in this file.  "distro" (str) represents distribution name. "source" (str) denotes source package name. "person_id" (str) indicates developer identity. "closes" (int), "high" (int),  "medium" (int), "low" (int) are the features.</li> <li>source_bugs.csv: In this file, three columns are present. "distro" (str) represents the distribution name. "source" (str) represents the source package name. "bug_count" (int) denotes the number of bugs that source package has at a particular distribution.</li> <li>source_sizes.csv: In this file, three columns are present. "distro" (str) represents the distribution name. "source" (str) represents source package name. "size" (int) denotes the size of the package.</li> <li>Dependency folder: Within this folder, ten dependency lists are present. Each file contains two columns i.e "start" (str) and "target" (str). Both of them represent source packages. So, we read as the "start" source package depends on "target" source package. </li> </ul> Here is the arxiv version of our paper: <a href="https://arxiv.org/abs/2101.08729">https://arxiv.org/abs/2101.08729</a>.  Here is the portal link: <a href="https://sites.google.com/view/rima-hazra/swnet">https://sites.google.com/view/rima-hazra/swnet</a>

SNPs markers of Trypoxylus dichotomus developed by using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques

The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability and phylogeography of 53 specimens of Trypoxylus species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high-resolution single nucleotide polymorphisms (SNPs) for genotyping.

Factors associated with patient satisfaction towards pharmacy services among out-patients attending public health clinics: Questionnaire development and its application

Introduction: Patient satisfaction is widely used to measure quality of healthcare by identifying potential areas for improvement. Aim of study is to assess patient satisfaction towards pharmacy services and its associated factors using newly developed questionnaire among outpatients attending public health clinics. Materials and Methods: Public Health Clinic Patient Satisfaction Questionnaire (PHC-PSQ) towards pharmacy services was developed using exploratory factor analysis and Cronbach's α. A cross-sectional study was conducted among 400 patients visiting the pharmacy in three randomly selected public health clinics recruited via systematic random sampling. Data was collected using a set of questionnaire including PHC-PSQ. Factors associated with patient satisfaction was analysed using multiple linear regression. Results: Final PHC-PSQ consisted of three domains (administrative competency, technical competency and convenience of location) and 22 items with 69.9% total variance explained. Cronbach's α for total items was 0.96. Total mean score for patient satisfaction was 7.56 (SD 1.32). Older age and higher education were associated with lower patient satisfaction mean score. Patients who had visited the pharmacy more than once in the past three months, perceived to be in better health status and had a more correct general knowledge of pharmacists expressed higher patient satisfaction mean score. Conclusions: PHC-PSQ is a newly developed tool to measure patient satisfaction towards pharmacy services in public health clinics in Malaysia. Patient satisfaction was relatively high. Age, education, frequency of visit, self-perceived health status and general knowledge of pharmacists were factors significantly associated with patient satisfaction.